MCscan - errors

[pauloizquierdo]

I am trying to run MCscan, but I got the following errors when I tried to download the data from phytozome:

[12:19:21] ERROR File .phytozome_directory_V12.xml exists. Download skipped. base.py:1417
Traceback (most recent call last):
File "/Users/paulo/miniconda3/lib/python3.9/runpy.py", line 197, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/Users/paulo/miniconda3/lib/python3.9/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/Users/paulo/.local/lib/python3.9/site-packages/jcvi/apps/fetch.py", line 726, in
main()
File "/Users/paulo/.local/lib/python3.9/site-packages/jcvi/apps/fetch.py", line 136, in main
p.dispatch(globals())
File "/Users/paulo/.local/lib/python3.9/site-packages/jcvi/apps/base.py", line 110, in dispatch
globalsaction
File "/Users/paulo/.local/lib/python3.9/site-packages/jcvi/apps/fetch.py", line 278, in phytozome
genomes = g.get_genomes()
File "/Users/paulo/.local/lib/python3.9/site-packages/jcvi/apps/biomart.py", line 34, in get_genomes
root = PhytozomePath(next(self.iter(tag="organismDownloads")))
File "/Users/paulo/.local/lib/python3.9/site-packages/jcvi/apps/biomart.py", line 69, in init
for child in element.getchildren():
AttributeError: 'xml.etree.ElementTree.Element' object has no attribute 'getchildren'

any idea why I got these errors?

Thanks

[pauloizquierdo]

The problem was LaTeX

[songjuntae2022]

File "/Users/paulo/.local/lib/python3.9/site-packages/jcvi/apps/biomart.py", line 69, in init
for child in element.getchildren():
AttributeError: 'xml.etree.ElementTree.Element' object has no attribute 'getchildren'

I solved it by replacing element.getchildren with list(element).

And the latex problem was solved by removing texlive-core installed from conda and installing texlive using apt-get.